Description
This track displays variants identified by Gire et al. in 81 isolates
from the 2014 strain of Ebola virus (78 from Sierra Leone and 3 from Guinea)
that are specific to the 2014 strain. At least one 2014 isolate carries a base not found
elsewhere in the EBOV alignment.
Display Conventions
Items are labeled by ancestral nucleotide and 2014-derived nucleotide.
Non-coding variants are black, synonymous variants are green,
and missense variants are red and also labeled by gene and amino acid change.
Click on an item to view more details such as the derived allele frequency
in 2014 isolates and, for missense changes, the
BLOSUM62 substitution score.
Methods
Blood samples were collected from 78 patients at Kenema Government Hospital
in Sierra Leone. For details of RNA preservation, PCR, human RNA depletion,
library construction and sequencing, see Supplemental Materials and Methods
of Gire et al.
Gire et al. analyzed the 78 Sierra Leone patient sequences together with
3 sequences from the 2014 outbreak in Guinea (Baize et al.;
suspected sequencing errors were masked, see Supplemental Materials and Methods of
Gire et al.), for a total of 81 sequences from 2014.
In addition, some analyses included 20 sequences from past outbreaks of Zaire Ebola
virus, 1976-2008, for a total of 101 sequences. Sequence variants were extracted
directly from multiple sequence alignments of the group of 101 sequences (1976-2014).
A custom release of
SnpEff
(v4.0, build 2014-07-01, to support ribosomal slippage in transcription of GP gene)
was used to predict functional effect of variants on genes (noncoding, synonymous
or missense).
References
Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N, Soropogui B, Sow MS,
Keïta S, De Clerck H et al.
Emergence of Zaire Ebola virus disease in Guinea.
N Engl J Med. 2014 Oct 9;371(15):1418-25.
PMID: 24738640
Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M,
Fullah M, Dudas G et al.
Genomic surveillance elucidates Ebola virus origin and transmission
during the 2014 outbreak.
Science 2014 Sep 12;345(6202):1369-72.
PMID: 25214632
Supplemental Materials and Methods
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